示例#1
0
文件: cgf.go 项目: abeconnelly/cgf
func print_zipper(sglf cglf.SGLF, allele_path [][]TileInfo) {

	var ok bool

	var path0 int
	var path1 int

	var step_idx0 int
	var step_idx1 int

	var step0 int
	var step1 int

	sglf_info0 := cglf.SGLFInfo{}
	sglf_info1 := cglf.SGLFInfo{}

	tile_zipper := make([][]cglf.SGLFInfo, 2)
	tile_zipper_seq := make([][]string, 2)

	span_sum := 0

	for (step_idx0 < len(allele_path[0])) && (step_idx1 < len(allele_path[1])) {

		if span_sum >= 0 {
			ti0 := allele_path[0][step_idx0]

			// sglf_info1 only holds a valid path and step
			//
			if step_idx0 > 0 {
				sglf_info0, ok = sglf.PfxTagLookup[ti0.PfxTag]
			} else {
				sglf_info0, ok = sglf.SfxTagLookup[ti0.SfxTag]
			}

			if !ok {
				log.Fatal("could not find prefix (%s) in sglf (allele_idx %d, step_idx %d (%x))\n",
					ti0.PfxTag, 0, step_idx0, step_idx0)
			}

			path0 = sglf_info0.Path
			step0 = sglf_info0.Step

			// We need to search for the variant in the Lib to find
			// the rest of the information, including span
			//
			var_idx0, e := lookup_variant_index(ti0.Seq, sglf.Lib[path0][step0])
			if e != nil {
				log.Fatal(e)
			}

			sglf_info0 = sglf.LibInfo[path0][step0][var_idx0]

			span0 := sglf_info0.Span

			sglf_info0.Variant = var_idx0

			seq0 := sglf.Lib[path0][step0][var_idx0]
			tile_zipper[0] = append(tile_zipper[0], sglf_info0)
			tile_zipper_seq[0] = append(tile_zipper_seq[0], seq0)

			span_sum -= span0
			step_idx0++

		} else {
			ti1 := allele_path[1][step_idx1]

			// sglf_info1 only holds a valid path and step
			//
			if step_idx1 > 0 {
				sglf_info1, ok = sglf.PfxTagLookup[ti1.PfxTag]
			} else {
				sglf_info1, ok = sglf.SfxTagLookup[ti1.SfxTag]
			}

			if !ok {
				log.Fatal("could not find prefix (%s) in sglf (allele_idx %d, step_idx %d (%x))\n",
					ti1.PfxTag, 1, step_idx1, step_idx1)
			}

			path1 = sglf_info1.Path
			step1 = sglf_info1.Step

			// We need to search for the variant in the Lib to find
			// the rest of the information, including span
			//
			var_idx1, e := lookup_variant_index(ti1.Seq, sglf.Lib[path1][step1])
			if e != nil {
				log.Fatal(e)
			}

			sglf_info1 = sglf.LibInfo[path1][step1][var_idx1]

			sglf_info1.Variant = var_idx1

			seq1 := sglf.Lib[path1][step1][var_idx1]
			tile_zipper[1] = append(tile_zipper[1], sglf_info1)
			tile_zipper_seq[1] = append(tile_zipper_seq[1], seq1)

			span1 := sglf_info1.Span

			span_sum += span1
			step_idx1++

		}

		if span_sum == 0 {

			fmt.Printf("[{a}")
			for i := 0; i < len(tile_zipper[0]); i++ {
				nocall_str0 := nocall_string(tile_zipper_seq[0][i])
				fmt.Printf(" %04x.00.%04x.%03x+%x;%s",
					tile_zipper[0][i].Path,
					tile_zipper[0][i].Step,
					tile_zipper[0][i].Variant,
					tile_zipper[0][i].Span,
					nocall_str0)
			}
			fmt.Printf(" ]\n")

			fmt.Printf("[{b}")
			for i := 0; i < len(tile_zipper[1]); i++ {
				nocall_str1 := nocall_string(tile_zipper_seq[1][i])
				fmt.Printf(" %04x.00.%04x.%03x+%x;%s",
					tile_zipper[1][i].Path,
					tile_zipper[1][i].Step,
					tile_zipper[1][i].Variant,
					tile_zipper[1][i].Span,
					nocall_str1)

			}
			fmt.Printf(" ]\n")
			fmt.Printf("\n")

			tile_zipper[0] = tile_zipper[0][0:0]
			tile_zipper[1] = tile_zipper[1][0:0]

			tile_zipper_seq[0] = tile_zipper_seq[0][0:0]
			tile_zipper_seq[1] = tile_zipper_seq[1][0:0]

		}

	}

}
示例#2
0
// Will overwrite cgf path structure if it exists, create a new path if it doesn't.
// It will create a new PathStruct if one doesn't already exist.
//
//func update_vector_path_simple(ctx *CGFContext, path_idx int, allele_path [][]TileInfo) error {
func (ctx *CGFContext) UpdateVectorPathSimple(path_idx int, allele_path [][]TileInfo) error {
	cgf := ctx.CGF
	sglf := ctx.SGLF

	//DEBUG
	//fmt.Printf("INTERMEDIATE\n")
	//emit_intermediate(ctx, path_idx, allele_path)
	//path_bytes,err := emit_path_bytes(ctx, path_idx, allele_path)
	path_bytes, err := ctx.EmitPathBytes(path_idx, allele_path)
	_ = path_bytes
	_ = err

	if err != nil {
		return err
	}

	g_debug := false

	if len(cgf.Path) < path_idx {
		tpath := make([]PathStruct, path_idx-len(cgf.Path)+1)
		cgf.Path = append(cgf.Path, tpath...)

		if g_debug {
			fmt.Printf(">>>>> len cgf.Path %d, path_idx %d\n", len(cgf.Path), path_idx)
		}
	}

	var ok bool

	var path0 int
	var path1 int

	var step_idx0 int
	var step_idx1 int

	var step0 int
	var step1 int

	// Overflow tier of variants.
	// These are variants that can't fit
	// into the packed vector but still
	// appear in the tile map.
	//
	overflow := OverflowStruct{}
	overflow.Stride = 256
	overflow.Offset = make([]uint64, 0, 16)
	overflow.Position = make([]uint64, 0, 16)
	overflow.Map = make([]byte, 0, 256)
	overflow_count := 0

	final_overflow := FinalOverflowStruct{}
	final_overflow.Stride = 256
	final_overflow.Offset = make([]uint64, 0, 16)
	final_overflow.Position = make([]uint64, 0, 16)
	final_overflow.DataRecord.Code = make([]byte, 0, 256)
	final_overflow.DataRecord.Data = make([]byte, 0, 2048)
	final_overflow_count := 0
	_ = final_overflow

	loq_info := LowQualityInfoStruct{}
	_ = loq_info

	buf := make([]byte, 1024)

	//sglf_info0 := SGLFInfo{}
	//sglf_info1 := SGLFInfo{}

	sglf_info0 := cglf.SGLFInfo{}
	sglf_info1 := cglf.SGLFInfo{}

	//tile_zipper := make([][]SGLFInfo, 2)
	tile_zipper := make([][]cglf.SGLFInfo, 2)
	tile_zipper_seq := make([][]string, 2)

	span_sum := 0

	var_a0 := make([]int, 0, 16)
	var_a1 := make([]int, 0, 16)

	span_a0 := make([]int, 0, 16)
	span_a1 := make([]int, 0, 16)

	ivec := make([]int, 0, 1024*16)

	anchor_step := 0
	update_anchor := true
	end_check := false
	loq_tile := false

	step_idx_info_for_loq := make([][]int, 2)
	step_idx_info_for_loq[0] = make([]int, 0, 1024)
	step_idx_info_for_loq[1] = make([]int, 0, 1024)

	loq_byte_length := uint64(0)
	loq_bytes := make([]byte, 0, 1024)

	loq_offset_bytes := make([]byte, 0, 1024)
	_ = loq_offset_bytes
	loq_position_bytes := make([]byte, 0, 1024)
	_ = loq_position_bytes
	loq_hom_flag_bytes := make([]byte, 0, 1024)
	_ = loq_hom_flag_bytes

	// We might need to fill this in after the fact
	//
	loq_offset := make([]uint64, 0, 1024)
	_ = loq_offset
	loq_position := make([]uint64, 0, 1024)
	_ = loq_position
	loq_hom_flag := make([]bool, 0, 1024)

	loq_count := uint64(0)
	loq_stride := uint64(256)

	cur_hexit_count := 0

	// First is allele
	// second is 3 element (varid,span,start,len)
	//
	//AlleleNocallInfo := make([][]int, 2)
	//

	//for (step_idx0<len(allele_path[0])) && (step_idx1<len(allele_path[1])) {
	for (step_idx0 < len(allele_path[0])) || (step_idx1 < len(allele_path[1])) {

		end_check = false

		if span_sum >= 0 {
			ti0 := allele_path[0][step_idx0]

			if len(ti0.NocallStartLen) > 0 {
				loq_tile = true
			}

			step_idx_info_for_loq[0] = append(step_idx_info_for_loq[0], step_idx0)

			// sglf_info1 only holds a valid path and step
			//
			if step_idx0 > 0 {
				sglf_info0, ok = sglf.PfxTagLookup[ti0.PfxTag]
			} else {
				sglf_info0, ok = sglf.SfxTagLookup[ti0.SfxTag]
			}

			if !ok {
				return fmt.Errorf("could not find prefix (%s) in sglf (allele_idx %d, step_idx %d (%x))\n",
					ti0.PfxTag, 0, step_idx0, step_idx0)
			}

			path0 = sglf_info0.Path
			step0 = sglf_info0.Step

			if update_anchor {
				anchor_step = step0
				update_anchor = false
			}

			// We need to search for the variant in the Lib to find
			// the rest of the information, including span
			//
			var_idx0, e := lookup_variant_index(ti0.Seq, sglf.Lib[path0][step0])
			if e != nil {
				return e
			}

			sglf_info0 = sglf.LibInfo[path0][step0][var_idx0]

			span0 := sglf_info0.Span

			sglf_info0.Variant = var_idx0

			seq0 := sglf.Lib[path0][step0][var_idx0]
			tile_zipper[0] = append(tile_zipper[0], sglf_info0)
			tile_zipper_seq[0] = append(tile_zipper_seq[0], seq0)

			var_a0 = append(var_a0, var_idx0)
			span_a0 = append(span_a0, span0)

			allele_path[0][step_idx0].VarId = var_idx0

			span_sum -= span0
			step_idx0++

		} else {
			ti1 := allele_path[1][step_idx1]

			if len(ti1.NocallStartLen) > 0 {
				loq_tile = true
			}

			step_idx_info_for_loq[1] = append(step_idx_info_for_loq[1], step_idx1)

			// sglf_info1 only holds a valid path and step
			//
			if step_idx1 > 0 {
				sglf_info1, ok = sglf.PfxTagLookup[ti1.PfxTag]
			} else {
				sglf_info1, ok = sglf.SfxTagLookup[ti1.SfxTag]
			}

			if !ok {
				return fmt.Errorf("could not find prefix (%s) in sglf (allele_idx %d, step_idx %d (%x))\n",
					ti1.PfxTag, 1, step_idx1, step_idx1)
			}

			path1 = sglf_info1.Path
			step1 = sglf_info1.Step

			// We need to search for the variant in the Lib to find
			// the rest of the information, including span
			//
			var_idx1, e := lookup_variant_index(ti1.Seq, sglf.Lib[path1][step1])
			if e != nil {
				return e
			}

			sglf_info1 = sglf.LibInfo[path1][step1][var_idx1]

			sglf_info1.Variant = var_idx1

			seq1 := sglf.Lib[path1][step1][var_idx1]
			tile_zipper[1] = append(tile_zipper[1], sglf_info1)
			tile_zipper_seq[1] = append(tile_zipper_seq[1], seq1)

			span1 := sglf_info1.Span

			var_a1 = append(var_a1, var_idx1)
			span_a1 = append(span_a1, span1)

			allele_path[1][step_idx1].VarId = var_idx1

			span_sum += span1
			step_idx1++

		}

		if span_sum == 0 {

			// =====================
			// =====================
			// ---------------------
			// STORE LOQ INFORMATION
			//

			if loq_tile {
				buf := make([]byte, 16)
				var dn int

				if (loq_count % loq_stride) == 0 {
					tobyte64(buf, uint64(len(loq_bytes)))
					loq_offset_bytes = append(loq_offset_bytes, buf[0:8]...)

					tobyte64(buf, uint64(anchor_step))
					loq_position_bytes = append(loq_position_bytes, buf[0:8]...)
				}
				loq_count++

				hom_flag := true
				if len(step_idx_info_for_loq[0]) != len(step_idx_info_for_loq[1]) {
					hom_flag = false
				} else {
					for ii := 0; ii < len(step_idx_info_for_loq[0]); ii++ {
						step_idx0 := step_idx_info_for_loq[0][ii]
						step_idx1 := step_idx_info_for_loq[1][ii]

						step0 := allele_path[0][step_idx0].Step
						step1 := allele_path[1][step_idx1].Step

						if step0 != step1 {
							hom_flag = false
							break
						}

						if len(allele_path[0][step_idx0].NocallStartLen) != len(allele_path[1][step_idx1].NocallStartLen) {
							hom_flag = false
							break
						}

						for jj := 0; jj < len(allele_path[0][step_idx0].NocallStartLen); jj++ {

							if allele_path[0][step_idx0].NocallStartLen[jj] != allele_path[1][step_idx1].NocallStartLen[jj] {
								hom_flag = false
								break
							}

						}
					}
				}

				loq_hom_flag = append(loq_hom_flag, hom_flag)

				// (NTile)
				// Number of tile in this record
				//
				dn = dlug.FillSliceUint64(buf, uint64(len(step_idx_info_for_loq[0])))
				loq_bytes = append(loq_bytes, buf[0:dn]...)

				if !hom_flag {

					// (NTile) (B allele)
					// Number of Allele B tiles in this record
					//
					dn = dlug.FillSliceUint64(buf, uint64(len(step_idx_info_for_loq[1])))
					loq_bytes = append(loq_bytes, buf[0:dn]...)

					//fmt.Printf("++ Ballele %d\n", len(step_idx_info_for_loq[1]))

				}

				for i := 0; i < len(step_idx_info_for_loq[0]); i++ {
					step_idx0 := step_idx_info_for_loq[0][i]
					ti := allele_path[0][step_idx0]

					// (LoqTile[].Len)
					// Number of noc entries for this tile
					//
					dn = dlug.FillSliceUint64(buf, uint64(len(ti.NocallStartLen)/2))
					loq_bytes = append(loq_bytes, buf[0:dn]...)

					prev_start := 0
					for jj := 0; jj < len(ti.NocallStartLen); jj += 2 {

						// (LoqTile[].LoqEntry[].DelPos)
						// Start position
						//
						dn = dlug.FillSliceUint64(buf, uint64(ti.NocallStartLen[jj]-prev_start))
						loq_bytes = append(loq_bytes, buf[0:dn]...)

						// (LoqTile[].LoqEntry[].LoqLen)
						// Length of noc
						//
						dn = dlug.FillSliceUint64(buf, uint64(ti.NocallStartLen[jj+1]))
						loq_bytes = append(loq_bytes, buf[0:dn]...)

						prev_start = ti.NocallStartLen[jj]
					}
				}

				if !hom_flag {

					for i := 0; i < len(step_idx_info_for_loq[1]); i++ {
						step_idx1 := step_idx_info_for_loq[1][i]
						ti := allele_path[1][step_idx1]

						// (LoqTile[].Len)
						// Number of noc entries
						//
						dn = dlug.FillSliceUint64(buf, uint64(len(ti.NocallStartLen)/2))
						loq_bytes = append(loq_bytes, buf[0:dn]...)

						prev_start := 0
						for jj := 0; jj < len(ti.NocallStartLen); jj += 2 {

							// (LoqTile[].LoqEntry[].DelPos)
							// Start of nocall
							//
							dn = dlug.FillSliceUint64(buf, uint64(ti.NocallStartLen[jj]-prev_start))
							loq_bytes = append(loq_bytes, buf[0:dn]...)

							// (LoqTile[].LoqEntry[].LoqLen)
							// Noc length
							//
							dn = dlug.FillSliceUint64(buf, uint64(ti.NocallStartLen[jj+1]))
							loq_bytes = append(loq_bytes, buf[0:dn]...)

							prev_start = ti.NocallStartLen[jj]

						}
					}

				}

			}

			//
			// STORE LOQ INFORMATION
			// ---------------------
			// =====================
			// =====================

			end_check = true

			tilemap_key := create_tilemap_string_lookup2(var_a0, span_a0, var_a1, span_a1)

			if g_debug {
				fmt.Printf(">> (%d,%x) {%v,%v} {%v,%v} %s\n",
					anchor_step, anchor_step,
					var_a0, span_a0, var_a1, span_a1,
					tilemap_key)
			}

			n := len(ivec)

			// Fill in spanning
			//
			for ; n <= anchor_step; n++ {
				ivec = append(ivec, -1)

				OVERFLOW_INDICATOR_SPAN_VALUE := 1025

				if (n % 32) == 0 {
					cur_hexit_count = 0
				}
				cur_hexit_count++
				if cur_hexit_count >= (32 / 4) {
					PathOverflowAdd(&overflow, overflow_count, anchor_step, OVERFLOW_INDICATOR_SPAN_VALUE)
					overflow_count++
				}

			}

			final_overflow_flag := true
			tilemap_pos := len(ctx.TileMapLookup)
			if _, ok := ctx.TileMapLookup[tilemap_key]; ok {
				final_overflow_flag = false
				tilemap_pos = ctx.TileMapPosition[tilemap_key]
			}

			if (!loq_tile) && (tilemap_pos < 13) && (cur_hexit_count < (32 / 4)) {

				// It's not a low quality tile and it can fit in a hexit
				//
				ivec[anchor_step] = tilemap_pos

				if (anchor_step % 32) == 0 {
					cur_hexit_count = 0
				}
				if cur_hexit_count >= (32 / 4) {
					PathOverflowAdd(&overflow, overflow_count, anchor_step, tilemap_pos)
					overflow_count++
					cur_hexit_count++
				}

			} else {

				// It's overflown.
				// If the entry doesn't appear in the tile map, the tilemap_pos
				// will be set to the length of the tilemap (e.g. 1024) as an indicator
				// that the final overflow table should be consulted for the entry
				//

				// overflow
				//
				if loq_tile {
					ivec[anchor_step] = -254
				} else {
					ivec[anchor_step] = 254
				}

				// --------
				// OVERFLOW
				//

				if (anchor_step % 32) == 0 {
					cur_hexit_count = 0
				}

				PathOverflowAdd(&overflow, overflow_count, anchor_step, tilemap_pos)

				overflow_count++
				cur_hexit_count++

				//
				// OVERFLOW
				// --------

			}

			if final_overflow_flag {

				//final overflow
				//
				if loq_tile {
					ivec[anchor_step] = -255
				} else {
					ivec[anchor_step] = 255
				}

				// --------------
				// FINAL OVERFLOW
				//

				// We haven't found the TileMap entry, so store the entry
				// here.
				// TODO: store raw sequence if it's not found in the Tile Library
				//

				p := final_overflow_count
				if (uint64(p) % overflow.Stride) == 0 {
					//final_overflow.Offset = append(final_overflow.Offset, uint64(len(final_overflow.Offset)))
					final_overflow.Offset = append(final_overflow.Offset, uint64(len(final_overflow.DataRecord.Data)))
					//final_overflow.Position = append(final_overflow.Position, uint64(final_overflow_count))
					final_overflow.Position = append(final_overflow.Position, uint64(anchor_step))
				}

				final_overflow.DataRecord.Code = append(final_overflow.DataRecord.Code, uint8(1))

				dn := dlug.FillSliceUint64(buf, uint64(len(var_a0)))
				final_overflow.DataRecord.Data = append(final_overflow.DataRecord.Data, buf[:dn]...)

				dn = dlug.FillSliceUint64(buf, uint64(len(var_a1)))
				final_overflow.DataRecord.Data = append(final_overflow.DataRecord.Data, buf[:dn]...)

				for ii := 0; ii < len(var_a0); ii++ {
					dn = dlug.FillSliceUint64(buf, uint64(var_a0[ii]))
					final_overflow.DataRecord.Data = append(final_overflow.DataRecord.Data, buf[:dn]...)

					dn = dlug.FillSliceUint64(buf, uint64(span_a0[ii]))
					final_overflow.DataRecord.Data = append(final_overflow.DataRecord.Data, buf[:dn]...)
				}

				for ii := 0; ii < len(var_a1); ii++ {
					dn = dlug.FillSliceUint64(buf, uint64(var_a1[ii]))
					final_overflow.DataRecord.Data = append(final_overflow.DataRecord.Data, buf[:dn]...)

					dn = dlug.FillSliceUint64(buf, uint64(span_a1[ii]))
					final_overflow.DataRecord.Data = append(final_overflow.DataRecord.Data, buf[:dn]...)
				}

				final_overflow_count++

				//
				// FINAL OVERFLOW
				// --------------

			}

			var_a0 = var_a0[0:0]
			var_a1 = var_a1[0:0]

			span_a0 = span_a0[0:0]
			span_a1 = span_a1[0:0]

			update_anchor = true

			tile_zipper[0] = tile_zipper[0][0:0]
			tile_zipper[1] = tile_zipper[1][0:0]

			tile_zipper_seq[0] = tile_zipper_seq[0][0:0]
			tile_zipper_seq[1] = tile_zipper_seq[1][0:0]

			loq_tile = false

			step_idx_info_for_loq[0] = step_idx_info_for_loq[0][0:0]
			step_idx_info_for_loq[1] = step_idx_info_for_loq[1][0:0]

		}

	}

	if !end_check {
		return fmt.Errorf("There are trailing tiles that could not be matched up")
	}

	if g_debug {
		for i := 0; i < len(ivec); i++ {
			fmt.Printf("[%d] %d\n", i, ivec[i])
		}
	}

	// Now we know the final size of the overflow structures so
	// fill in their length
	//

	/*
	  overflow.Length = 8 + 8 +
	    uint64(len(overflow.Offset)*8) +
	    uint64(len(overflow.Position)*8) +
	    uint64(len(overflow.Map))
	*/
	overflow.Length = uint64(overflow_count)

	// Add in final byte position of Map
	//if int( (uint64(len(overflow.Offset)) + overflow.Stride - 1) / overflow.Stride ) > len(overflow.Offset) {
	if (overflow.Length % overflow.Stride) != 0 {
		overflow.Offset = append(overflow.Offset, uint64(len(overflow.Map)))
	}

	/*
	  final_overflow.Length = 8 + 8 +
	    uint64(len(final_overflow.Offset)*8) +
	    uint64(len(final_overflow.Position)*8) +
	    uint64(len(final_overflow.DataRecord.Code)) +
	    uint64(len(final_overflow.DataRecord.Data))
	*/
	final_overflow.Length = uint64(final_overflow_count)

	// Add in final byte position of Map
	//if int( (uint64(len(final_overflow.Offset)) + final_overflow.Stride - 1) / final_overflow.Stride ) > len(final_overflow.Offset) {
	if (final_overflow.Length % final_overflow.Stride) != 0 {
		final_overflow.Offset = append(final_overflow.Offset, uint64(len(final_overflow.DataRecord.Data)))
	}

	packed_len := (len(ivec) + 31) / 32
	packed_vec := make([]uint64, packed_len)

	for i := 0; i < (packed_len - 1); i++ {

		hexit_ovf_count := uint(0)
		for jj := 0; jj < 32; jj++ {

			ivec_pos := 32*i + jj

			if ivec[ivec_pos] == 0 {
				continue
			}
			packed_vec[i] |= (1 << (32 + uint(jj)))

			// 32/4 hexits available
			// fill in from right to left
			//
			if hexit_ovf_count < (32 / 4) {

				if ivec[ivec_pos] == -1 {

					// spanning tile, 0 hexit

				} else if (ivec[ivec_pos] == 255) || (ivec[ivec_pos] == 254) {

					// hiq overflow
					//
					packed_vec[i] |= (0xf << (4 * hexit_ovf_count))

				} else if (ivec[ivec_pos] == -255) || (ivec[ivec_pos] == -254) {

					// loq overflow
					//
					packed_vec[i] |= (0xe << (4 * hexit_ovf_count))

				} else if ivec[ivec_pos] == 256 {

					// complex
					//
					packed_vec[i] |= (0xd << (4 * hexit_ovf_count))

				} else {

					// otherwise we can encode the tile lookup in the hexit
					//
					//packed_vec[i] |= (uint64(ivec[ivec_pos]&0xff)<<(4*hexit_ovf_count))
					packed_vec[i] |= (uint64(ivec[ivec_pos]&0xf) << (4 * hexit_ovf_count))

				}

			}

			hexit_ovf_count++

		}

	}

	fin_loq_bytes := make([]byte, 0, 1024)

	//TODO:
	// final packed bit vector population

	if g_debug {
		for i := 0; i < len(packed_vec); i++ {
			fmt.Printf("[%d,%x (%d)] |%8x|%8x|\n", 32*i, 32*i, i, packed_vec[i]>>32, packed_vec[i]&0xffffffff)
		}

		fmt.Printf("\n\n")
		fmt.Printf("Overflow.Length: %d (0x%x)\n", overflow.Length, overflow.Length)
		fmt.Printf("Overflow.Stride: %d\n", overflow.Stride)
		fmt.Printf("Overflow.Offset:")
		for ii := 0; ii < len(overflow.Offset); ii++ {
			fmt.Printf("  [%d] %d\n", ii, overflow.Offset[ii])
		}
		fmt.Printf("\n")

		fmt.Printf("Overflow.Position:")
		for ii := 0; ii < len(overflow.Position); ii++ {
			fmt.Printf("  [%d] %d\n", ii, overflow.Position[ii])
		}

		idx := 0
		for b_offset := 0; b_offset < len(overflow.Map); {
			tm, dn := dlug.ConvertUint64(overflow.Map[b_offset:])

			fmt.Printf("  [%d] %d (0x%x)\n", idx, tm, tm)

			b_offset += dn
			idx++
		}

		fmt.Printf("\n\n")
		fmt.Printf("FinalOverflow.Length: %d (0x%x)\n", final_overflow.Length, final_overflow.Length)
		fmt.Printf("FinalOverflow.Stride: %d\n", final_overflow.Stride)
		fmt.Printf("FinalOverflow.Offset:\n")
		for ii := 0; ii < len(final_overflow.Offset); ii++ {
			fmt.Printf("  [%d] %d\n", ii, final_overflow.Offset[ii])
		}
		fmt.Printf("\n")

		fmt.Printf("FinalOverflow.Position:\n")
		for ii := 0; ii < len(final_overflow.Position); ii++ {
			fmt.Printf("  [%d] %d\n", ii, final_overflow.Position[ii])
		}
		fmt.Printf("\n")

		fmt.Printf("FinalOverflow.DataRecord:\n")

		byte_map_offset := 0
		for ii := 0; ii < len(final_overflow.DataRecord.Code); ii++ {
			fmt.Printf("  [%d] Code: %d, Data:", ii, final_overflow.DataRecord.Code[ii])

			if final_overflow.DataRecord.Code[ii] == 1 {
				n0, dn := dlug.ConvertUint64(final_overflow.DataRecord.Data[byte_map_offset:])
				byte_map_offset += dn

				n1, dn := dlug.ConvertUint64(final_overflow.DataRecord.Data[byte_map_offset:])
				byte_map_offset += dn

				fmt.Printf(" (%d,%d)", n0, n1)

				fmt.Printf(" [")
				for jj := uint64(0); jj < n0; jj++ {

					vid, dn := dlug.ConvertUint64(final_overflow.DataRecord.Data[byte_map_offset:])
					byte_map_offset += dn

					span, dn := dlug.ConvertUint64(final_overflow.DataRecord.Data[byte_map_offset:])
					byte_map_offset += dn

					fmt.Printf(" %x+%x", vid, span)
				}
				fmt.Printf(" ]")

				fmt.Printf(" [")
				for jj := uint64(0); jj < n1; jj++ {

					vid, dn := dlug.ConvertUint64(final_overflow.DataRecord.Data[byte_map_offset:])
					byte_map_offset += dn

					span, dn := dlug.ConvertUint64(final_overflow.DataRecord.Data[byte_map_offset:])
					byte_map_offset += dn

					fmt.Printf(" %x+%x", vid, span)
				}
				fmt.Printf(" ]")

				fmt.Printf("\n")

			} else {
				panic("unsupported")
			}

		}

		// -------------

		var byt byte
		for i := 0; i < len(loq_hom_flag); i++ {
			if (i > 0) && ((i % 8) == 0) {
				loq_hom_flag_bytes = append(loq_hom_flag_bytes, byt)
				byt = 0
			}

			if loq_hom_flag[i] {
				byt |= (1 << uint8(i%8))
			}
		}
		if len(loq_hom_flag) > 0 {
			loq_hom_flag_bytes = append(loq_hom_flag_bytes, byt)
		}

		fmt.Printf("# loq_bytes(%d)", len(loq_bytes))

		// Create final low quality information
		//
		//fin_loq_bytes := make([]byte, 0, 1024)

		loq_byte_length = 0
		loq_byte_length += 8 // length (this field)
		loq_byte_length += 8 // NRecord
		loq_byte_length += 8 // code
		loq_byte_length += 8 // stride
		loq_byte_length += uint64(len(loq_offset_bytes))
		loq_byte_length += uint64(len(loq_position_bytes))
		loq_byte_length += uint64(len(loq_hom_flag_bytes))
		loq_byte_length += uint64(len(loq_bytes))

		tobyte64(buf, loq_byte_length)
		fin_loq_bytes = append(fin_loq_bytes, buf[0:8]...)

		tobyte64(buf, uint64(loq_count))
		fin_loq_bytes = append(fin_loq_bytes, buf[0:8]...)

		code := uint64(0)
		tobyte64(buf, code)
		fin_loq_bytes = append(fin_loq_bytes, buf[0:8]...)

		stride := uint64(256)
		tobyte64(buf, stride)
		fin_loq_bytes = append(fin_loq_bytes, buf[0:8]...)

		fin_loq_bytes = append(fin_loq_bytes, loq_offset_bytes...)
		fin_loq_bytes = append(fin_loq_bytes, loq_position_bytes...)
		fin_loq_bytes = append(fin_loq_bytes, loq_hom_flag_bytes...)

		fin_loq_bytes = append(fin_loq_bytes, loq_bytes...)

		for i := 0; i < len(fin_loq_bytes); i++ {
			if (i % 16) == 0 {
				fmt.Printf("\n")
			}
			fmt.Printf(" %2x", fin_loq_bytes[i])
		}
		fmt.Printf("\n")

		print_low_quality_information(fin_loq_bytes)

		//DEBUG
		//err := ioutil.WriteFile("./loq_bytes.bin", fin_loq_bytes, 0644)
		//if err!=nil { panic(err); }

	}

	ctx.CGF.Path[path_idx].Name = fmt.Sprintf("%04x", path_idx)
	ctx.CGF.Path[path_idx].Vector = packed_vec
	ctx.CGF.Path[path_idx].Overflow = overflow
	ctx.CGF.Path[path_idx].FinalOverflow = final_overflow
	ctx.CGF.Path[path_idx].LowQualityBytes = fin_loq_bytes

	return nil

}